The goal of the project is to develop a general optical imaging technology for studying vital small bio-molecules (e.g., amino acids, nucleic acids, fatty acids, glucose, neurotransmitters and drugs) inside live cells and tissues, an important but otherwise intractable goal. To do so, we propose to couple the emerging stimulated Raman scattering (SRS) microscopy, which is capable of producing concentration maps of chemical bonds in biological samples, with three distinct classes of small vibrational tags with characteristic Raman transitions, including alkyne moieties (i.e., CC triple bond), deuterium isotope and 13C isotope. While alkyne tags are generally applicable to any small biomolecules, deuterium isotope and 13C isotope will be particularly useful for labeling amino acids. When spectrally targeting these vibrational tags labeled to small bio-molecules, SRS microscopy is ideally suited for probing functional metabolism of living systems at microscopic level, as proved in our recent publications. We have laid out systematic plans as to how to crystallize this concept into a mature and general technical platform. Accompanied by the technical development, several biomedical applications are being proposed (some with exciting preliminary data) including imaging neurogenesis in living brain tissues by monitoring the metabolic incorporation of alkyne-tagged deoxyribonucleoside into newly born neurons, multicolor chemical imaging by developing a color palette of metabolite library, monitoring protein synthesis in nervous systems with deuterium-labeled amino acids, and probing intracellular protein degradation during Huntingtin aggregation with 13C-labeled phenylalanine. If successfully implemented, we will establish a new imaging platform of bioorthogonal nonlinear Raman microscopy that could allow us to interrogate a broad spectrum of small bio-molecules with superb sensitivity, specificity, biocompatibility and multiplex ability. The resulting bioorthogonal nonlinear Raman microscopy might do for small bio-molecules what fluorescence imaging of organic dyes and fluorescent proteins has done for larger molecular species, bringing small bio-molecules under the illumination of modern light microscopy.